Sun Oct 9 12:31:17 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 12:31:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6956657 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -4.781000 44.14300 ymin,ymax (A): -14.02700 37.14700 zmin,zma (A): 1.846000 44.37500 x,y,z range (A): 48.92400 51.17400 42.52900 scale (grids/A): 0.6956657 object centre (A): 19.68100 11.56000 23.11050 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500025 assigned positive charge : 369.6591 centred at (gu) : 89.23651 90.96104 90.91396 assigned negative charge : -366.1595 centred at (gu) : 89.19751 91.15163 91.01118 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7801 nv = 96 ne = 84 npr = 48385 no. pairs analyzed = 48385 no. exposed pairs = 2964 no. arc points = 20700 no. surface atoms = 992 nbur = 1410 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4357 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.1800000 number of dielectric boundary points 3841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1903 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5491132E-08 -2.4000238E-08 midg,1,midg; midg,igrid,midg 8.8101388E-08 -7.6091681E-08 1,midg,midg; igrid,midg,midg 7.3289930E-09 3.5349366E-08 gauss-seidel spectral radius is 0.9892634 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 12:31:17 rms-change max change #iterations 0.2095935 30.24197 at 10iterations 2.5906766E-02 3.416595 at 20iterations 3.7013546E-03 0.5869598 at 30iterations 8.4068417E-04 0.1410141 at 40iterations 2.7657169E-04 4.5253754E-02 at 50iterations finished qdiffx linear iterations at : 12:31:20 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.7657169E-04 4.5253754E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 12:31:20 3.348u 0.168s 0:03.84 91.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 12:31:21 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.086997 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -4.781000 44.14300 ymin,ymax (A): -14.02700 37.14700 zmin,zma (A): 1.846000 44.37500 x,y,z range (A): 48.92400 51.17400 42.52900 scale (grids/A): 2.086997 object centre (A): 19.68100 11.56000 23.11050 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500025 assigned positive charge : 369.6591 centred at (gu) : 87.70908 92.88277 92.74142 assigned negative charge : -366.1595 centred at (gu) : 87.59215 93.45458 93.03353 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20700 grid for indexing accessible points = 1.400000 m= 31513 mr = 58269 m= 5535 mr = 23505 m= 460 mr = 3515 m= 15 mr = 247 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1054 time to turn everything in is 0.4100000 number of dielectric boundary points 35023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17926 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6956657 object centre at (A) : 19.68100 11.56000 23.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4428061E-02 1.8215649E-03 midg,1,midg; midg,igrid,midg 2.1870403E-02 -7.7152736E-02 1,midg,midg; igrid,midg,midg 5.6082133E-02 5.6218435E-03 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.6300000 now iterating at: 12:31:21 rms-change max change #iterations 4.971748 224.9996 at 10iterations 2.441837 83.69894 at 20iterations 1.209664 38.88548 at 30iterations 0.6012130 17.74704 at 40iterations 0.2982320 8.601748 at 50iterations 0.1483499 4.426619 at 60iterations 7.3528692E-02 2.161758 at 70iterations 3.6629152E-02 1.073608 at 80iterations 1.8341100E-02 0.5282445 at 90iterations 9.2874179E-03 0.2771111 at 100iterations 4.7488497E-03 0.1416941 at 110iterations 2.5118047E-03 8.1947327E-02 at 120iterations finished qdiffx linear iterations at : 12:31:28 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 2.5118047E-03 8.1947327E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 12:31:29 7.882u 0.190s 0:08.35 96.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 12:31:29 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.130496 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -4.781000 44.14300 ymin,ymax (A): -14.02700 37.14700 zmin,zma (A): 1.846000 44.37500 x,y,z range (A): 48.92400 51.17400 42.52900 scale (grids/A): 3.130496 object centre (A): 19.68100 11.56000 23.11050 number of atom coordinates read : 2402 total number of charged atoms : 2260 net assigned charge : 3.500025 assigned positive charge : 369.6591 centred at (gu) : 86.56351 94.32409 94.11201 assigned negative charge : -366.1595 centred at (gu) : 86.38813 95.18185 94.55027 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 191417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20700 grid for indexing accessible points = 1.400000 m= 100501 mr = 140287 m= 38196 mr = 82987 m= 10126 mr = 30929 m= 1872 mr = 7648 m= 247 mr = 1367 m= 9 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 3426 time to turn everything in is 1.240000 number of dielectric boundary points 78991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 18078 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.086997 object centre at (A) : 19.68100 11.56000 23.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6192275 -9.0435021E-02 midg,1,midg; midg,igrid,midg 0.4927984 -0.7717221 1,midg,midg; igrid,midg,midg 0.8013903 -0.1485898 gauss-seidel spectral radius is 0.9993003 estimated iterations to convergence 298 setup time was (sec) 1.480000 now iterating at: 12:31:31 rms-change max change #iterations 11.08443 390.4209 at 10iterations 6.569662 132.0506 at 20iterations 3.878907 75.70386 at 30iterations 2.289161 44.97500 at 40iterations 1.350342 27.49595 at 50iterations 0.7941091 16.15594 at 60iterations 0.4656741 8.293812 at 70iterations 0.2734791 4.887267 at 80iterations 0.1602921 2.893114 at 90iterations 9.4036452E-02 1.575483 at 100iterations 5.5225849E-02 0.8809711 at 110iterations 3.2578819E-02 0.5527039 at 120iterations 1.9381195E-02 0.3414745 at 130iterations 1.1662136E-02 0.2121429 at 140iterations 7.1963952E-03 0.1331024 at 150iterations 4.6315221E-03 9.6881866E-02 at 160iterations 3.1493818E-03 6.6055298E-02 at 170iterations 2.2826393E-03 4.8881531E-02 at 180iterations finished qdiffx linear iterations at : 12:31:42 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 2.2826393E-03 4.8881531E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 12:31:42 12.988u 0.212s 0:13.47 97.9% 0+0k 0+0io 0pf+0w